Quantification of UV-induced cyclobutane pyrimidine dimers using an oligonucleotide chip assay
A lesion-specific enzyme-induced DNA strand break assay was developed for an oligonucleotide chip for the determination of UVB-induced cyclobutane pyrimidine dimers (CPDs). A 20-mer of fluorophore-labeled and biotinylated oligonucleotide was immobilized on the chip. CPDs in DNA on the chip were form...
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| Veröffentlicht in: | Analytical and bioanalytical chemistry 2010-07, Vol.397 (6), p.2271-2277 |
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| creator | Kim, Min Jung Lee, Su Chul Kang, Seong Ho Choo, Jaebum Song, Joon Myong |
| description | A lesion-specific enzyme-induced DNA strand break assay was developed for an oligonucleotide chip for the determination of UVB-induced cyclobutane pyrimidine dimers (CPDs). A 20-mer of fluorophore-labeled and biotinylated oligonucleotide was immobilized on the chip. CPDs in DNA on the chip were formed by UVB irradiation (312 nm). T4 endonuclease V (T4N5) was used to excise the CPD site as T4N5 sensitively and specifically detects CPDs. The fluorophore-labeled DNA fragments were detected by a laser-induced fluorescence (LIF) detection system. The number of CPDs induced by UVB was determined based on a mathematical equation obtained from a predetermined calibration curve. The yield of UVB-induced CPDs was 1.73 CPDs per megabase per (kJ/m²). The reliability of this value was proved by its similarity to reference values obtained from gel electrophoresis. The developed assay has strong potential to quantify most kinds of UV-induced DNA lesions. |
| doi_str_mv | 10.1007/s00216-010-3793-6 |
| format | Article |
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A 20-mer of fluorophore-labeled and biotinylated oligonucleotide was immobilized on the chip. CPDs in DNA on the chip were formed by UVB irradiation (312 nm). T4 endonuclease V (T4N5) was used to excise the CPD site as T4N5 sensitively and specifically detects CPDs. The fluorophore-labeled DNA fragments were detected by a laser-induced fluorescence (LIF) detection system. The number of CPDs induced by UVB was determined based on a mathematical equation obtained from a predetermined calibration curve. The yield of UVB-induced CPDs was 1.73 CPDs per megabase per (kJ/m²). The reliability of this value was proved by its similarity to reference values obtained from gel electrophoresis. The developed assay has strong potential to quantify most kinds of UV-induced DNA lesions.</description><identifier>ISSN: 1618-2642</identifier><identifier>EISSN: 1618-2650</identifier><identifier>DOI: 10.1007/s00216-010-3793-6</identifier><identifier>PMID: 20473657</identifier><language>eng</language><publisher>Berlin/Heidelberg: Berlin/Heidelberg : Springer-Verlag</publisher><subject>Analytical Chemistry ; Assaying ; Biochemistry ; Biotin ; Calibration ; Carbocyclic compounds ; Characterization and Evaluation of Materials ; Chemistry ; Chemistry and Materials Science ; Chips ; Cyclobutane ; Cyclobutane pyrimidine dimer ; Deoxyribonuclease (Pyrimidine Dimer) - metabolism ; Detectors ; Dimers ; DNA ; DNA Breaks - radiation effects ; DNA Damage - genetics ; Enzymes ; Exact sciences and technology ; Fluorescence ; Fluorescent Dyes ; Food Science ; Laboratory Medicine ; Lesion-specific enzyme-induced break assay ; Mathematical analysis ; Monitoring/Environmental Analysis ; Oligonucleotide Array Sequence Analysis - methods ; Oligonucleotide Array Sequence Analysis - standards ; Oligonucleotide chip ; Oligonucleotides ; Pyrimidine Dimers - analysis ; Pyrimidine Dimers - radiation effects ; Pyrimidines ; Short Communication ; Spectrometric and optical methods ; T4 endonuclease V ; Ultraviolet Rays - adverse effects ; Viral Proteins - metabolism</subject><ispartof>Analytical and bioanalytical chemistry, 2010-07, Vol.397 (6), p.2271-2277</ispartof><rights>Springer-Verlag 2010</rights><rights>2015 INIST-CNRS</rights><rights>COPYRIGHT 2010 Springer</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c501t-3017f2f738c55e224db192f85f40f49b8e928873e8b9d7e672ae4fe328e1c8463</citedby><cites>FETCH-LOGICAL-c501t-3017f2f738c55e224db192f85f40f49b8e928873e8b9d7e672ae4fe328e1c8463</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00216-010-3793-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00216-010-3793-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23004778$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20473657$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kim, Min Jung</creatorcontrib><creatorcontrib>Lee, Su Chul</creatorcontrib><creatorcontrib>Kang, Seong Ho</creatorcontrib><creatorcontrib>Choo, Jaebum</creatorcontrib><creatorcontrib>Song, Joon Myong</creatorcontrib><title>Quantification of UV-induced cyclobutane pyrimidine dimers using an oligonucleotide chip assay</title><title>Analytical and bioanalytical chemistry</title><addtitle>Anal Bioanal Chem</addtitle><addtitle>Anal Bioanal Chem</addtitle><description>A lesion-specific enzyme-induced DNA strand break assay was developed for an oligonucleotide chip for the determination of UVB-induced cyclobutane pyrimidine dimers (CPDs). 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The developed assay has strong potential to quantify most kinds of UV-induced DNA lesions.</description><subject>Analytical Chemistry</subject><subject>Assaying</subject><subject>Biochemistry</subject><subject>Biotin</subject><subject>Calibration</subject><subject>Carbocyclic compounds</subject><subject>Characterization and Evaluation of Materials</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Chips</subject><subject>Cyclobutane</subject><subject>Cyclobutane pyrimidine dimer</subject><subject>Deoxyribonuclease (Pyrimidine Dimer) - metabolism</subject><subject>Detectors</subject><subject>Dimers</subject><subject>DNA</subject><subject>DNA Breaks - radiation effects</subject><subject>DNA Damage - genetics</subject><subject>Enzymes</subject><subject>Exact sciences and technology</subject><subject>Fluorescence</subject><subject>Fluorescent Dyes</subject><subject>Food Science</subject><subject>Laboratory Medicine</subject><subject>Lesion-specific enzyme-induced break assay</subject><subject>Mathematical analysis</subject><subject>Monitoring/Environmental Analysis</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Oligonucleotide Array Sequence Analysis - standards</subject><subject>Oligonucleotide chip</subject><subject>Oligonucleotides</subject><subject>Pyrimidine Dimers - analysis</subject><subject>Pyrimidine Dimers - radiation effects</subject><subject>Pyrimidines</subject><subject>Short Communication</subject><subject>Spectrometric and optical methods</subject><subject>T4 endonuclease V</subject><subject>Ultraviolet Rays - adverse effects</subject><subject>Viral Proteins - metabolism</subject><issn>1618-2642</issn><issn>1618-2650</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkUtv1TAQhSMEoqXwA9hANhVsUvy2s6wqHpUqVRVclliOMw6uEvtiJ4v773GUS9lVlRce2d85nvGpqrcYXWCE5KeMEMGiQRg1VLa0Ec-qUyywaojg6PlDzchJ9Srne4QwV1i8rE4IYpIKLk-rX3eLCbN33prZx1BHV-9-Nj70i4W-tgc7xm6ZTYB6f0h-8r0vZe8nSLlesg9DbYpo9EMMix0hzr6H2v72-9rkbA6vqxfOjBneHPezavfl84-rb83N7dfrq8ubxnKE54YiLB1xkirLORDC-g63xCnuGHKs7RS0RClJQXVtL0FIYoA5oEQBtooJelZ92Hz3Kf5ZIM968tnCOJbO45K15GVcysUTSEoFkZzRQn58lMSSMSFW24JebOhgRtA-uDgnY8vqYfI2BnC-nF_StkVlVL52gTeBTTHnBE7vy--adNAY6TVbvWWrS7Z6zVavmnfHfpZugv5B8S_MApwfAZOtGV0ywfr8n6OokFIVjmxcLldhgKTv45JCyefR199vImeiNkMqxrvvBOEyjxJEYUn_Av6YxAI</recordid><startdate>20100701</startdate><enddate>20100701</enddate><creator>Kim, Min Jung</creator><creator>Lee, Su Chul</creator><creator>Kang, Seong Ho</creator><creator>Choo, Jaebum</creator><creator>Song, Joon Myong</creator><general>Berlin/Heidelberg : Springer-Verlag</general><general>Springer-Verlag</general><general>Springer</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>L7M</scope><scope>7X8</scope><scope>7QH</scope><scope>7UA</scope><scope>C1K</scope></search><sort><creationdate>20100701</creationdate><title>Quantification of UV-induced cyclobutane pyrimidine dimers using an oligonucleotide chip assay</title><author>Kim, Min Jung ; Lee, Su Chul ; Kang, Seong Ho ; Choo, Jaebum ; Song, Joon Myong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c501t-3017f2f738c55e224db192f85f40f49b8e928873e8b9d7e672ae4fe328e1c8463</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Analytical Chemistry</topic><topic>Assaying</topic><topic>Biochemistry</topic><topic>Biotin</topic><topic>Calibration</topic><topic>Carbocyclic compounds</topic><topic>Characterization and Evaluation of Materials</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Chips</topic><topic>Cyclobutane</topic><topic>Cyclobutane pyrimidine dimer</topic><topic>Deoxyribonuclease (Pyrimidine Dimer) - metabolism</topic><topic>Detectors</topic><topic>Dimers</topic><topic>DNA</topic><topic>DNA Breaks - radiation effects</topic><topic>DNA Damage - genetics</topic><topic>Enzymes</topic><topic>Exact sciences and technology</topic><topic>Fluorescence</topic><topic>Fluorescent Dyes</topic><topic>Food Science</topic><topic>Laboratory Medicine</topic><topic>Lesion-specific enzyme-induced break assay</topic><topic>Mathematical analysis</topic><topic>Monitoring/Environmental Analysis</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Oligonucleotide Array Sequence Analysis - standards</topic><topic>Oligonucleotide chip</topic><topic>Oligonucleotides</topic><topic>Pyrimidine Dimers - analysis</topic><topic>Pyrimidine Dimers - radiation effects</topic><topic>Pyrimidines</topic><topic>Short Communication</topic><topic>Spectrometric and optical methods</topic><topic>T4 endonuclease V</topic><topic>Ultraviolet Rays - adverse effects</topic><topic>Viral Proteins - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kim, Min Jung</creatorcontrib><creatorcontrib>Lee, Su Chul</creatorcontrib><creatorcontrib>Kang, Seong Ho</creatorcontrib><creatorcontrib>Choo, Jaebum</creatorcontrib><creatorcontrib>Song, Joon Myong</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><collection>Aqualine</collection><collection>Water Resources Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><jtitle>Analytical and bioanalytical chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kim, Min Jung</au><au>Lee, Su Chul</au><au>Kang, Seong Ho</au><au>Choo, Jaebum</au><au>Song, Joon Myong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantification of UV-induced cyclobutane pyrimidine dimers using an oligonucleotide chip assay</atitle><jtitle>Analytical and bioanalytical chemistry</jtitle><stitle>Anal Bioanal Chem</stitle><addtitle>Anal Bioanal Chem</addtitle><date>2010-07-01</date><risdate>2010</risdate><volume>397</volume><issue>6</issue><spage>2271</spage><epage>2277</epage><pages>2271-2277</pages><issn>1618-2642</issn><eissn>1618-2650</eissn><abstract>A lesion-specific enzyme-induced DNA strand break assay was developed for an oligonucleotide chip for the determination of UVB-induced cyclobutane pyrimidine dimers (CPDs). A 20-mer of fluorophore-labeled and biotinylated oligonucleotide was immobilized on the chip. CPDs in DNA on the chip were formed by UVB irradiation (312 nm). T4 endonuclease V (T4N5) was used to excise the CPD site as T4N5 sensitively and specifically detects CPDs. The fluorophore-labeled DNA fragments were detected by a laser-induced fluorescence (LIF) detection system. The number of CPDs induced by UVB was determined based on a mathematical equation obtained from a predetermined calibration curve. The yield of UVB-induced CPDs was 1.73 CPDs per megabase per (kJ/m²). The reliability of this value was proved by its similarity to reference values obtained from gel electrophoresis. The developed assay has strong potential to quantify most kinds of UV-induced DNA lesions.</abstract><cop>Berlin/Heidelberg</cop><pub>Berlin/Heidelberg : Springer-Verlag</pub><pmid>20473657</pmid><doi>10.1007/s00216-010-3793-6</doi><tpages>7</tpages></addata></record> |
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| subjects | Analytical Chemistry Assaying Biochemistry Biotin Calibration Carbocyclic compounds Characterization and Evaluation of Materials Chemistry Chemistry and Materials Science Chips Cyclobutane Cyclobutane pyrimidine dimer Deoxyribonuclease (Pyrimidine Dimer) - metabolism Detectors Dimers DNA DNA Breaks - radiation effects DNA Damage - genetics Enzymes Exact sciences and technology Fluorescence Fluorescent Dyes Food Science Laboratory Medicine Lesion-specific enzyme-induced break assay Mathematical analysis Monitoring/Environmental Analysis Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Array Sequence Analysis - standards Oligonucleotide chip Oligonucleotides Pyrimidine Dimers - analysis Pyrimidine Dimers - radiation effects Pyrimidines Short Communication Spectrometric and optical methods T4 endonuclease V Ultraviolet Rays - adverse effects Viral Proteins - metabolism |
| title | Quantification of UV-induced cyclobutane pyrimidine dimers using an oligonucleotide chip assay |
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